DL_POLY is a package of subroutines, programs and data files, designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems and solutions on a distributed memory parallel computer. DL_POLY was developed at the STFC Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. Three versions of DL_POLY are currently available:
DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors.
DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.
DL_POLY_4's general design provides scalable performance from a single processor workstation to a high performance parallel computer. DL_POLY_4 offers fully parallel I/O as well as a netCDF alternative (HDF5 library dependence) to the default ASCII trajectory file. It is also available as a CUDA+OpenMP port, developed in collaboration with ICHEC, to harness the power offered by NVIDIA® GPUs. A full description of the available DL_POLY_4 functionality may be obtained from the DL_POLY_4 User Manual (PDF).
Currently, only one version of the DL_POLY software is available under an STFC license, DL_POLY_4, and with support provisioned to the UK's academia only. The former DL_POLY_2 version (authored by W. Smith, T.R. Forester and I.T. Todorov) is now transformed into DL_POLY_CLASSIC and available as open source under the BSD license.
Users should express their interest to the Helpdesk to gain access to the executables.
To use a version of DL_POLY on Fionn load the relevant environment module:
module load dlpoly/4.09
Assuming that the following SLURM script is saved as dlpoly.sub, the job can be submitted to the queue by running the following command in the same directory:
Job Submission Example on Fionn
#!/bin/sh # All the information about queues can be obtained using 'sinfo' # PARTITION AVAIL TIMELIMIT # DevQ up 1:00:00 # ProdQ* up 3-00:00:00 # LongQ up 6-00:00:00 # ShmemQ up 3-00:00:00 # PhiQ up 1-00:00:00 # GpuQ up 2-00:00:00 # Slurm flags #SBATCH -p ProdQ #SBATCH -N 1 #SBATCH -t 02:00:00 #SBATCH --job-name=dlpolyJob # Charge job to myproject #SBATCH -A MyProject # Write stdout+stderr to file #SBATCH -o output.txt # Mail me on job start & end #SBATCH --mail-user=myEmail@domain.ie #SBATCH --mail-type=BEGIN,END cd $SLURM_SUBMIT_DIR module load dlpoly/4.09 mpirun -np 4 DLPOLY.Z > output
More information can be obtained here.